Chromatin, the physiological template of genetic information in eukaryotes, is subject to distinct posttranslational modifications on histone N-terminal regions (tails). Lysine methylation contributes to a histone code that extends the information in the genetic code. A number of distinct methylation marks dictate transition between transcriptionally active and silent chromatin states. Chromo (chromatin organization modifier) domains are protein modules that recognize lysine methylation marks on histones tails. Recently, we reported two structures, 1) The complex of Heterochromatin Protein-1 (HP1) chromodomain with a lysine- 9 methylated histone H3 tail and 2) The complex of Polycomb chromodomain with a lysine-27 methylated histone H3 tail. These structures suggested that an aromatic cage in the chromodomain forms pi-cation interactions with the methylammonium group of the modified lysine. To better understand the diverse mechanisms by which other chromodomains discriminate methyllysines in the context of alternate histone sequences, we propose to characterize the structure of 3 other chromodomain complexes with their target histone H3 and H4 peptides. The chromodomain of CHD1 chromo-ATPase/helicases-DNA-binding 1), CMT3 (chromo methyl transferase 3) and MSL3 (male-specific lethal 3) proteins will be studied by NMR spectroscopy, X-ray crystallography, fluorescence anisotropy and isothermal titration calorimetry. A subset of chromodomains does not have a conserved aromatic cage and binds RNA. To understand the mechanism by which these chromodomains interact with RNA, we propose to characterize the structure of 2 other chromodomain complexes: the chromodomain of CHD1 and MOF (male absent on the first). These studies will contribute to our understanding of chromodomain function in 3 distinct epigenetic regulation pathways: a) transcriptional elongation by the CHD1 protein, b) DNA cytosine methylation by the CMT3 protein and c) X-chromosome dosage compensation by the MSL3 and MOF proteins.